Would it be possible for you to deposit this repo at zenodo or figshare or similar so it can get a DOI? I want to cite it in a paper (as a shining example of using R pkgs as research compendia) and would prefer to have a DOI specifically for this repo (rather than the publication) for the authoritative version of the code. Thanks!

You can replace the first page of your code (loading packages) with pacman::p_load.

E.g. pacman::p_load("dplyr", "ggplot2", "lubridate").
The packages will be installed if they are not available.

Need to dig through and tell a story

Use predict() with new data set to orig data and predict.all = TRUE

• Get sessionInfo() working
• Clean up Table 4. Hard to read now.

Play around with pandoc template and abstract placement.

See if you can place abstract at end of Rmd and have it render up front in final pdf by using \begin{abstract}\end{abstract}.

If this works you can create abstract after all code chunks and use objects created in those within the body of the abstract.

Review and delete my notes in the body of the text

• Figure 1: color code dots by Trophic State?
• Figures 4 & 7: add ug/l to the y-label or mention in caption. What about the units on the X axis. Alternatively, all units could be specified in the appendix.
• Figures 7 and 13-need to add the names of the ecoregions since they are mentioned in the text. Alternatively they could be shown in a new table or in the body of text.
• Figures 8 & 9: need legend or specify in caption All Var=Red and GIS=Black
• Figure 9: is the Y axis label term "conditional total accuracy" defined in the text?
• Figure 10: the subpanels (maps),need to be larger. Consider using the same color scale for all and Figure 11 also.
• Table 1: add ug/l to the column heading "concentration cut-off"
• Tables 2 & 3 add the "Predicted" over column labels and "Observed" next to row labels.
• Appendix: add units and summary stats column-Mean and SE if not more.

need to update some of the citations.

1.) Read et al NLA paper

Results-change 5 to 6

Figure formatting details listed on page 9 of http://esapubs.org/esapubs/ESPFinal.pdf